Background: A growing literature describes the importance of social-emotional learning (SEL) for student social behavior, academic performance, and emotional health. One widely implemented school program, the Quiet Time program, has been shown to improve factors associated with SEL, including positive emotional and behavioral coping skills, resilience, and self-actualization. Methods: A total of 101 sixth-grade students, 51 students from a public West Coast Quiet Time school practicing Transcendental Meditation (TM) and 50 non-meditating students from a matched-control school, participated in the study. Both teacher rating of social-emotional competencies, using the Devereux Student Strengths Assessment (DESSA), and student self-reported psychological distress, using the Strengths and Difficulties Questionnaire (SDQ) emotional symptoms scale, were completed at baseline and four-month posttest. Results: Significant improvement was found in the TM group compared to controls in social-emotional competencies for both the entire sample and high-risk subgroup (p values <0.001; effect sizes = 0.78 and 1.32, respectively). A decrease in negative emotional symptoms was observed in high-risk TM students compared to controls (p < 0.073; effect size = -0.70). Conclusion: These findings indicate the value of implementing TM to enhance social-emotional learning and decrease psychological distress in middle school students. Future studies are encouraged.